Microscopic hematuria is being increasingly recognized as a major indicator of kidney deterioration. Persistent hematuria may better detect estimated glomerular filtration rate (eGFR) deterioration and potential glomerulonephritis. We conducted a retrospective cohort study to investigate the associations between persistent hematuria: the frequency or consistency of positive dipstick hematuria defined by the preceding 3 years urinalyses, and eGFR deterioration over 5 years and abnormal urinalyses suggesting potential glomerulonephritis (hematuria 1+ or higher, 2+ or higher, proteinuria, and hematuria and proteinuria) 5 years later, among adult participants with positive dipstick hematuria at baseline in a large-scale Japanese health checkup setting (n = 2104). There was no significant association between persistent hematuria and eGFR deterioration over 5 years. The higher the frequency of preceding hematuria, the greater the RR of hematuria 5 years later; RRs of hematuria with preceding thrice, twice, or once hematuria were 3.64 [95% CI, 3.11–4.25], 2.97 [95% CI, 2.52–3.51], or 1.91 [95% CI, 1.58–2.30] for “hematuria 1+ or higher,” and 7.13 [95% CI, 5.17–9.83], 4.26 [95% CI, 3.02–6.02], or 2.23 [95% CI, 1.52–3.27] for “hematuria 2+ or higher”. The presence of both hematuria and proteinuria 5 years later was only associated with preceding thrice hematuria (RR: 2.35 [95% CI, 1.37–4.03]). In conclusion, persistent hematuria for 3 years was associated with hematuria and proteinuria that were suggesting glomerulonephritis, but not associated with eGFR deterioration over 5 years. Multiple dipstick urinalyses over years can add some values to detect potential glomerulonephritis as an early sign of chronic kidney diseases.