var organizations = from org in db.Organizations
where org.Divisions.Count > 0
select org;

Debug.WriteLine(organizations);

will output:

SELECT [t0].[OrganizationID], [t0].[Name]
FROM [dbo].[Organizations] AS [t0]
WHERE ((
SELECT COUNT(*)
FROM [dbo].[Divisions] AS [t1]
WHERE [t1].[OrganizationID] = [t0].[OrganizationID]
)) > @p0