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Background Clinical high risk (CHR) for psychosis is a heterogeneous syndrome presenting with highly variable clinical symptoms and cognitive dysfunctions. This study investigated whether subtypes defined by clinical and cognitive features in the initial presentation in CHR might improve the prediction of psychosis. Methods From the ongoing ShangHai at Risk for Psychosis (SHARP) program, a total of 400 CHR subjects were enrolled in a prospective cohort study. Canonical correlation analysis (CCA) was applied to 289 CHR subjects with completed structured interviews for prodromal symptoms and MATRICS consensus cognitive battery tests at baseline, and at least 1-year follow-up. Canonical variates were generated by CCA and then used for hierarchical cluster analysis to produce subtypes. To test further the utility of 3 subtypes in predicting psychosis, Kaplan-Meyer survival curves were constructed from the 3 subtypes. Results CCA determined two linear combinations: 1) Negative symptom and functional deterioration-related cognitive features; and 2) Positive symptoms and emotional disorganization-related cognitive features. Cluster analysis revealed 3 subtypes defined by distinct and relatively homogeneous patterns along two dimensions, and comprising 14.2% (subtype-1, n=41), 37.4% (subtype-2, n=108), and 48.4% (subtype-3, n=140) of the sample, each with distinctive features of clinical and cognitive performance. Those with subtype-1, which is characterized by extensive negative symptoms and cognitive deficits, appear to have the highest risk for psychosis. The conversion risk for subtypes 1–3 are 39.0%, 11.1% and 18.6%, respectively. Discussion Our results define important subtypes within CHR syndromes that highlight clinical symptoms and cognitive features that transcend current diagnostic boundaries. The three different subtypes were associated with significant differences in their clinical and cognitive characteristics as well as in their risk of conversion to psychosis. [ABSTRACT FROM AUTHOR]