BACKGROUND Interpreting emotional expressions is a socio-cognitive skill central to interpersonal interaction. Poor emotion recognition has been reported in autism but is less well understood in other kinds of intellectual disabilities (ID), with procedural differences making comparisons across studies and syndromes difficult. This study aimed to compare directly facial emotion recognition skills in children with fragile X syndrome (FXS), Down's syndrome (DS) and non-specific intellectual disability (NSID), contrasting ability and error profiles with those of typically developing (TD) children of equivalent cognitive and linguistic status. METHODS Sixty children participated in the study: 15 FXS, 15 DS, 15 NSID and 15 TD children. Standardised measures of cognitive, language and socialisation skills were collected for all children, along with measures of performance on two photo-matching tasks: an 'identity-matching' task (to control for basic face-processing ability) and an 'emotion-matching' task (happiness, sadness, anger, surprise, fear or disgust). RESULTS Identity-matching ability did not differ across the four child groups. Only the DS group performed significantly more poorly on the emotion-matching task and only in comparison to the TD group, with fear recognition an area of particular difficulty. CONCLUSIONS Findings support previous evidence of emotion recognition abilities commensurate with overall developmental level in children with FXS or NSID, but not DS. They also suggest, however, that syndrome-specific difficulties may be subtle and detectable, at least in smaller-scale studies, only in comparison with TD matches, and not always across syndromes. Implications for behavioural phenotype theory, educational interventions and future research are discussed.