Prosody is a fundamental speech element responsible for communicative functions such as intonation, accent and phrasing, and prosodic impairments of individuals with intellectual disabilities reduce their communication skills. Yet, technological resources have paid little attention to prosody. This study aims to develop an automatic classifier to predict the prosodic quality of utterances produced by individuals with Down syndrome, and to analyse how inter-individual heterogeneity affects assessment results. A therapist and an expert in prosody judged the prosodic appropriateness of a corpus of Down syndrome' utterances collected through a video game. The judgments of the expert were used to train an automatic classifier that predicts prosodic quality by using a set of fundamental frequency, duration and intensity features. The classifier accuracy was 79.3% and its true positive rate 89.9%. We analyzed how informative each of the features was for the assessment and studied relationships between participants' developmental level and results: interspeaker variability conditioned the relative weight of prosodic features for automatic classification and participants' developmental level was related to the prosodic quality of their productions. Therefore, since speaker variability is an intrinsic feature of individuals with Down syndrome, it should be considered to attain an effective automatic prosodic assessment system.