Despite the operational criteria in diagnostic systems there is still marked diversity between clinical and research diagnoses in populations with psychotic disorders. The objective of the current study was to explore the association of patient-related factors with diagnostic agreement between clinical diagnoses and Schedules for Clinical Assessment in Neuropsychiatry (SCAN-2) diagnoses in first-episode psychosis. The sample included 80 consecutive patients. As explanatory variables we used demographic characteristics (gender, age, living circumstances, education, and social activities), measures of psychopathology (Positive and Negative Symptom scale [PANSS], Hamilton Depression Scale, Global Assessment of Functioning Scale [GAF], and Strauss-Carpenter Scale), duration of untreated psychosis, and diagnostic category according to SCAN-2 interview. The overall agreement value between the clinical and research diagnoses was 0.55 (kappa). In the whole sample low scores on the PANSS negative subscale, low level of education, and high score on the PANSS item for delusions predicted diagnostic discrepancy. Acute and transient psychotic disorder as a research diagnosis predicted diagnostic agreement. In the schizophrenia group, young age and lack of social activities predicted diagnostic agreement. Bivariate comparisons of treatment compliance, perceived medication side effects, or negative attitudes towards treatment showed no associations with diagnostic agreement. The results confirm some of the findings in the few previous studies. The diagnosis of schizophrenia is likely to be delayed and there is a need for further education with clinicians in recognizing the symptoms of schizophrenia.