Patients with schizophrenia have substantial comorbidity contributing to reduced life expectancy of 10-20 years. Identifying which comorbidities might be modifiable could improve rates of premature mortality in this population. We hypothesize that conditions that frequently co-occur but lack shared genetic risk with schizophrenia are more likely to be products of treatment, behavior, or environmental factors and therefore potentially modifiable. To test this hypothesis, we calculated phenome-wide comorbidity from electronic health records (EHR) in 250,000 patients in each of two independent health care institutions (Vanderbilt University Medical Center and Mass General Brigham) and association with schizophrenia polygenic risk scores (PRS) across the same phenotypes (phecodes) in linked biobanks. Comorbidity with schizophrenia was significantly correlated across institutions (r = 0.85) and consistent with prior literature. After multiple test correction, there were 77 significant phecodes comorbid with schizophrenia. Overall, comorbidity and PRS association were highly correlated (r = 0.55, p = 1.29×10-118), however, 36 of the EHR identified comorbidities had significantly equivalent schizophrenia PRS distributions between cases and controls. Fifteen of these lacked any PRS association and were enriched for phenotypes known to be side effects of antipsychotic medications (e.g., "movement disorders", "convulsions", "tachycardia") or other schizophrenia related factors such as from smoking ("bronchitis") or reduced hygiene (e.g., "diseases of the nail") highlighting the validity of this approach. Other phenotypes implicated by this approach where the contribution from shared common genetic risk with schizophrenia was minimal included tobacco use disorder, diabetes, and dementia. This work demonstrates the consistency and robustness of EHR-based schizophrenia comorbidities across independent institutions and with the existing literature. It identifies comorbidities with an absence of shared genetic risk indicating other causes that might be more modifiable and where further study of causal pathways could improve outcomes for patients.