Successful treatment of bladder cancer depends largely on early diagnosis of primary and recurrent disease. Sensitive, specific and noninvasive procedures for detection are especially needed for grade 1 and 2 bladder tumors, because of the relatively low sensitivity of cytology. Here we introduce a novel strategy to improve the sensitivity and reliability of microsatellite analyses by employing marker-specific threshold values for loss-of-heterozygosity (LOH) at 10 loci. These individual cut-offs were experimentally determined with 35 normal control tissues and subsequently validated in a retrospective study with bladder cancer biopsies from 86 patients. In a prospective analysis of voided urines samples and matched blood probes from 91 patients, LOH-analysis, UroVysion FISH and conventional urine cytology were compared with histological findings of consecutive transurethral biopsies. Whereas all samples could be analyzed by our LOH assay, only 56 samples were suitable for all 3 analyses. The highest sensitivity was obtained with our LOH-assay/cytology approach (G1-2: 72%; G3: 96%) being only surpassed by a combination of all 3 techniques (G1-2: 83%; G3: 100%). Since over 93% of the patients with recurrent disease were identified by LOH/cytology-analyses of their voided urine samples, a monitoring scheme alternating cystoscopy with LOH/cytology-examination could now be envisioned to reduce invasive interventions and consequently improve follow-up compliance, especially in patients with low grade tumors.