Background Patients with hypopituitarism have an increased mortality. The aim of this study was to investigate comorbidities including cerebral infarction, type 2 diabetes mellitus (T2DM) and malignant tumors in patients with non-functioning pituitary adenomas (NFPA) with and without growth hormone replacement therapy (GHRT). Methods Observational cohort study in patients with NFPA within the western region of Sweden. Subjects were identified through the National Patient Registry and followed between 1987 and 2014. Patient records were reviewed and standardized incidence ratios (SIRs) with 95% CIs for comorbidities were calculated. Results In total, 426 patients were included, 206 with GHRT and 219 without. Median (range) follow-up time for patients with and without GHRT was 12.2 (0–24) and 8.2 (0–27) years, respectively. Mean ± s.d. BMI was 28.5 ± 4.5 and 26.5 ± 4.4 for patients with and without GHRT, respectively (P < 0.001). Incidence of cerebral infarction was increased (SIR: 1.39; 95% CI: 1.03–1.84; P = 0.032), with no difference between patients with and without GHRT. SIR for T2DM in patients not receiving GHRT was increased (1.65; 1.06–2.46; P = 0.018), whereas the incidence in patients receiving GHRT was not (0.99; 0.55–1.63; P = 0.99). The incidence of malignant tumors was not increased, either in patients with or without GHRT. Conclusion The incidence of cerebral infarction is increased in patients with NFPA irrespective of GHRT. Patients without GHRT had an increased risk of T2DM, whereas patients with GHRT had a normal incidence of T2DM, despite having higher BMI. Incidence of malignant tumors was not increased. Thus, long-term GHRT seems to be safe regarding risk of comorbidities.