The present study investigated small molecule analysis of urinary samples as a noninvasive method to detect acute cellular renal allograft rejection. Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) was used to analyze 15 urinary samples from transplant patients with different grades of biopsy showing improved clinical acute cellular rejection (ACR) and 24 urinary samples from 8 transplant patients without evidence of rejection. Seven small molecules demonstrated highly successful diagnostic performance (m/z): 278.1 (t = 3.398, p = 0.004), 293.0 (t = 2.169, p = 0.048), 294.1 (t = 2.154, p = 0.05), 382.2 (t = 2.961, p = 0.010), 383.3 (t = 2.270, p = 0.040), 402.2 (t = 2.994, p = 0.010), 424.0 (t = 2.644, p = 0.019). Kidney transplant patients with ACR could be distinguished from those without ACR using four individual small molecules with a specificity of 100%. In conclusion, the combination of MALDI-FTMS technology with a clear definition of patient groups can detect urine small molecule associated with ACR.