Purpose: The purpose of this study was to investigate the processing of morphosyntactic cues (case and verb agreement) by children with cochlear implants (CIs) in German which-questions, where interpretation depends on these morphosyntactic cues. The aim was to examine whether children with CIs who perceive the different cues also make use of them in speech comprehension and processing in the same way as children with normal hearing (NH). Method: Thirty-three children with CIs (age 7;01-12;04 years; months, M = 9;07, bilaterally implanted before age 3;3) and 36 children with NH (age 7;05-10;09 years, M = 9;01) received a picture selection task with eye tracking to test their comprehension of subject, object, and passive "which-questions." Two screening tasks tested their auditory discrimination of case morphology and their perception and comprehension of subject-verb agreement. Results: Children with CIs who performed well on the screening tests still showed more difficulty on the comprehension of object questions than children with NH, whereas they comprehended subject questions and passive questions equally well as children with NH. There was large interindividual variability within the CI group. The gaze patterns of children with NH showed reanalysis effects for object questions disambiguated later in the sentence by verb agreement, but not for object questions disambiguated by case at the first noun phrase. The gaze patterns of children with CIs showed reanalysis effects even for object questions disambiguated at the first noun phrase. Conclusions: Even when children with CIs perceive case and subject-verb agreement, their ability to use these cues for offline comprehension and online processing still lags behind normal development, which is reflected in lower performance rates and longer processing times. Individual variability within the CI group can partly be explained by working memory and hearing age.