Schizophrenia (SCH) and drug addiction are chronic disorders that are frequently accompanied by physical diseases, poor nutrition and reduced self-care, all of which are likely to result in vitamin deficiencies. The objective of this study was to compare vitamin levels in SCH patients, substance use disorder (SUD) patients and healthy controls (HCs). The study included 189 SCH patients, 119 SUD patients and 109 HCs. Information on vitamin B12, folic acid and vitamin D levels were retrieved from the hospital’s database, and mean values and deficiency/insufficiency were evaluated. Vitamin D deficiency (<30 ng/ml) was more common in the SCH group than in the SUD and HC groups (88.4%, 74.8% and 86.4%, respectively). Although there were no significant differences in folic acid deficiency (<3.0 ng/ml) in the SUD and SCH groups (15.1% and 8.5%, respectively), the incidence of folic acid deficiency was significantly higher in both groups as compared with that in the HC group (5.8%). Significantly higher numbers of patients in the SCH group than in the SUD group had vitamin B12 deficiency (45.5% vs. 28.3%). The prevalence of vitamin B12 deficiency in the SUD group was significantly higher than that the HC group (28.3% vs.11.5%). As compared with the HC group, vitamin D and B12 levels were significantly lower in SCH group, and folic acid and B12 levels were significantly lower in the SUD group. Several vitamin deficiencies appear to be common in both SCH and SUD. Possible reasons should be investigated.