They had emerods in their secret (or hidden) parts That is, internally, in their hinder parts; which is the worst kind of emerods, as all physicians acknowledge, both because their pains are far more sharp than those of the other kind, and because the malady is more out of the reach of remedies.
Related Commentaries of 1 Samuel 5:9
1 Samuel 5:9
9 And it was so, that, after they had carried it about, the hand of the LORD was against the city with a very great destruction: and he smote the men of the city, both small and great, and they had emerods in their secret parts.