MySQL count occurrences greater than 2

To get a list of the words that appear more than once together with how often they occur, use a combination of GROUP BY and HAVING:

SELECT word, COUNT(*) AS cnt
FROM words
GROUP BY word
HAVING cnt > 1

To find the number of words in the above result set, use that as a subquery and count the rows in an outer query:

SELECT COUNT(*)
FROM
(
    SELECT NULL
    FROM words
    GROUP BY word
    HAVING COUNT(*) > 1
) T1