Background Few studies exist about risk factors for complications in subsequent biopsies. Purpose To explore risk factors for complications in initial versus subsequent biopsies in native and transplant kidneys, which may predict biopsy complications. Material and Methods In a multicenter study, 2830 native kidney biopsies (4.3% subsequent) were analyzed for major complications (1251 of these were also analyzed for minor) and 667 transplant kidney biopsies (29% subsequent) were analyzed for major and minor complications. No death or nephrectomy were described. Fisher’s exact test, Student’s t-test, chi-square analyses, and univariate and multiple binary logistic regression analyses were employed; P < 0.05 was considered significant. Results In initial native kidney biopsies, the frequency of major complications was higher in women compared to men (odds ratio 1.6, 95% confidence interval 1.1–2.2), in younger patients (50 vs. 54 years, P = 0.007), and in patients with lower weight (78 vs. 82 kg, P = 0.005). In subsequent native kidney biopsies, patients with major complications had a higher systolic blood pressure (145 vs. 132 mmHg, P = 0.03). In initial transplant kidney biopsies, biopsies with major complications had less glomeruli in the biopsy (17 vs. 24, P = 0.046). In subsequent transplant kidney biopsies, patients with major complications had a higher mean arterial pressure (112 vs. 98 mmHg, P = 0.002). In subsequent native kidney biopsies, there was a higher number of SLE-nephritis (12% vs. 4.6%, P = 0.001) compared to initial biopsies. Conclusion The different types of risk factors for complications in initial versus subsequent renal biopsies could be important for the clinicians to improve patients’ safety.