diff --git a/client/src/components/categorical/category.js b/client/src/components/categorical/category.js
index 45ac40cc..2353c729 100644
--- a/client/src/components/categorical/category.js
+++ b/client/src/components/categorical/category.js
@@ -27,10 +27,10 @@ class Category extends React.Component {
       const cat = categoricalSelection[metadataField];
       const categoryCount = {
         // total number of categories in this dimension
-        totalCatCount: cat.numCategories,
+        totalCatCount: cat.numCategoryValues,
         // number of selected options in this category
         selectedCatCount: _.reduce(
-          cat.categorySelected,
+          cat.categoryValueSelected,
           (res, cond) => (cond ? res + 1 : res),
           0
         )
@@ -91,7 +91,7 @@ class Category extends React.Component {
     const { categoricalSelection, metadataField } = this.props;
 
     const cat = categoricalSelection[metadataField];
-    const optTuples = sortedCategoryValues([...cat.categoryIndices]);
+    const optTuples = sortedCategoryValues([...cat.categoryValueIndices]);
     return _.map(optTuples, (tuple, i) => (
       <Value
         optTuples={optTuples}
diff --git a/client/src/components/categorical/value.js b/client/src/components/categorical/value.js
index bb16bb85..15c45d49 100644
--- a/client/src/components/categorical/value.js
+++ b/client/src/components/categorical/value.js
@@ -46,8 +46,8 @@ class CategoryValue extends React.Component {
     if (!categoricalSelection) return null;
 
     const category = categoricalSelection[metadataField];
-    const selected = category.categorySelected[categoryIndex];
-    const count = category.categoryCounts[categoryIndex];
+    const selected = category.categoryValueSelected[categoryIndex];
+    const count = category.categoryValueCounts[categoryIndex];
     const value = category.categoryValues[categoryIndex];
     const displayString = String(
       category.categoryValues[categoryIndex]
diff --git a/client/src/reducers/categoricalSelection.js b/client/src/reducers/categoricalSelection.js
index d7779d2c..af48a765 100644
--- a/client/src/reducers/categoricalSelection.js
+++ b/client/src/reducers/categoricalSelection.js
@@ -30,15 +30,15 @@ const CategoricalSelection = (
       /*
       Set the specific category in this field to false
       */
-      const newCategorySelected = Array.from(
-        state[action.metadataField].categorySelected
+      const newCategoryValueSelected = Array.from(
+        state[action.metadataField].categoryValueSelected
       );
-      newCategorySelected[action.categoryIndex] = true;
+      newCategoryValueSelected[action.categoryIndex] = true;
       const newCategoricalSelection = {
         ...state,
         [action.metadataField]: {
           ...state[action.metadataField],
-          categorySelected: newCategorySelected
+          categoryValueSelected: newCategoryValueSelected
         }
       };
       return newCategoricalSelection;
@@ -48,15 +48,15 @@ const CategoricalSelection = (
       /*
       Set the specific category in this field to false
       */
-      const newCategorySelected = Array.from(
-        state[action.metadataField].categorySelected
+      const newCategoryValueSelected = Array.from(
+        state[action.metadataField].categoryValueSelected
       );
-      newCategorySelected[action.categoryIndex] = false;
+      newCategoryValueSelected[action.categoryIndex] = false;
       const newCategoricalSelection = {
         ...state,
         [action.metadataField]: {
           ...state[action.metadataField],
-          categorySelected: newCategorySelected
+          categoryValueSelected: newCategoryValueSelected
         }
       };
       return newCategoricalSelection;
@@ -70,8 +70,9 @@ const CategoricalSelection = (
         ...state,
         [action.metadataField]: {
           ...state[action.metadataField],
-          categorySelected: Array.from(
-            state[action.metadataField].categorySelected
+          categorySelected: false,
+          categoryValueSelected: Array.from(
+            state[action.metadataField].categoryValueSelected
           ).fill(false)
         }
       };
@@ -86,8 +87,9 @@ const CategoricalSelection = (
         ...state,
         [action.metadataField]: {
           ...state[action.metadataField],
-          categorySelected: Array.from(
-            state[action.metadataField].categorySelected
+          categorySelected: true,
+          categoryValueSelected: Array.from(
+            state[action.metadataField].categoryValueSelected
           ).fill(true)
         }
       };
diff --git a/client/src/reducers/crossfilter.js b/client/src/reducers/crossfilter.js
index 7c8f66cc..4c8ea570 100644
--- a/client/src/reducers/crossfilter.js
+++ b/client/src/reducers/crossfilter.js
@@ -183,10 +183,12 @@ const CrossfilterReducer = (
     case "categorical metadata filter select":
     case "categorical metadata filter deselect": {
       const { categoricalSelection } = nextSharedState;
+      const { world } = prevSharedState;
       const cat = categoricalSelection[action.metadataField];
+      const col = world.obsAnnotations.col(action.metadataField);
       return state.select(obsAnnoDimensionName(action.metadataField), {
         mode: "exact",
-        values: ControlsHelpers.selectedValuesForCategory(cat)
+        values: ControlsHelpers.selectedValuesForCategory(cat, col)
       });
     }
 
diff --git a/client/src/util/stateManager/controlsHelpers.js b/client/src/util/stateManager/controlsHelpers.js
index fa5f1e82..27ecef46 100644
--- a/client/src/util/stateManager/controlsHelpers.js
+++ b/client/src/util/stateManager/controlsHelpers.js
@@ -21,16 +21,16 @@ Remember that option values can be ANY js type, except undefined/null.
   {
     _category_name_1: {
       // map of option value to index
-      categoryIndices: Map([
+      categoryValueIndices: Map([
         catval1: index,
         ...
       ])
 
       // index->selection true/false state
-      categorySelected: [ true/false, true/false, ... ]
+      categoryValueSelected: [ true/false, true/false, ... ]
 
       // number of options
-      numCategories: number,
+      numCategoryValues: number,
 
       // isTruncated - true if the options for selection has
       // been truncated (ie, was too large to implement)
@@ -65,18 +65,21 @@ export function createCategoricalSelection(maxCategoryItems, world) {
         key !== "name" &&
         summary.categories.length < maxCategoryItems;
       if (isSelectableCategory) {
-        const [categoryValues, categoryCounts] = topNCategories(summary);
-        const categoryIndices = new Map(categoryValues.map((v, i) => [v, i]));
-        const numCategories = categoryIndices.size;
-        const categorySelected = new Array(numCategories).fill(true);
+        const [categoryValues, categoryValueCounts] = topNCategories(summary);
+        const categoryValueIndices = new Map(
+          categoryValues.map((v, i) => [v, i])
+        );
+        const numCategoryValues = categoryValueIndices.size;
+        const categoryValueSelected = new Array(numCategoryValues).fill(true);
         const isTruncated = categoryValues.length < summary.numCategories;
         res[key] = {
           categoryValues, // array: of natively typed category values
-          categoryIndices, // map: category value (native type) -> category index
-          categorySelected, // array: t/f selection state
-          numCategories, // number: of categories
+          categoryValueIndices, // map: category value (native type) -> category index
+          categoryValueSelected, // array: t/f selection state
+          numCategoryValues, // number: of values in the category
           isTruncated, // bool: true if list was truncated
-          categoryCounts // array: cardinality of each category
+          categoryValueCounts, // array: cardinality of each category,
+          categorySelected: true // bool - default state for entire category
         };
       }
     }
@@ -88,12 +91,26 @@ export function createCategoricalSelection(maxCategoryItems, world) {
 given a categoricalSelection, return the list of all category values
 where selection state is true (ie, they are selected).
 */
-export function selectedValuesForCategory(categorySelectionState) {
-  const selectedValues = _([...categorySelectionState.categoryIndices])
-    .filter(tuple => categorySelectionState.categorySelected[tuple[1]])
-    .map(tuple => tuple[0])
-    .value();
-  return selectedValues;
+export function selectedValuesForCategory(categorySelectionState, dfColumn) {
+  const {
+    categorySelected,
+    categoryValueSelected,
+    categoryValueIndices
+  } = categorySelectionState;
+  let selectedValues;
+  if (categorySelected) {
+    selectedValues = new Set(dfColumn.summarize().categories);
+  } else {
+    selectedValues = new Set();
+  }
+  categoryValueIndices.forEach((catIndex, catValue) => {
+    if (!categoryValueSelected[catIndex]) {
+      selectedValues.delete(catValue);
+    } else {
+      selectedValues.add(catValue);
+    }
+  });
+  return [...selectedValues.values()];
 }
 
 /*