Male infertility (MI) accounts for at least 30% of infertility etiology, yet the full breadth of potential MI risk factors and adverse health outcomes has not been explored. Here, we use electronic medical records (EMRs) from the University of California (UC) and Stanford to implement a data-driven case-control study to identify MI-associated comorbidities. We identified 6,531 and 5,551 MI patients at UC and Stanford, respectively, as well as 8,353 and 2,464 vasectomy control patients at UC and Stanford, respectively. We used temporally-stratified logistic regression analyses to identify MI-associated comorbidities before or after 6 months after a patient’s first MI diagnosis or vasectomy-related record. We found 15 and 2 diagnoses positively associated with MI before and after the 6-month cutoff across both hospital systems and all analyses, respectively, including less expected comorbidities such as hypothyroidism and type 2 diabetes. Our findings can set the groundwork for future studies to clarify the relationship between less expected comorbidities and MI.