We disclose an in-toilet urinalysis system which includes a system for collection urine and for analysis of urine components using aptamer technology. Urine collection system may dispense urine into cuvettes, channels, or other containers that include aptamers. The aptamers may detect target molecules in urine. The aptamers may measure urine analytes, detect excreted drugs or drug metabolites, or disease markers. Upon binding to the target molecule, the aptamers may produce a signal which a sensor in the toilet may detect. In some embodiments, the signal may be electrochemical, fluorescent, or colorimetric. The measurements obtained from analysis of the urine may be used to assess a user's health or diagnose disease. In some embodiments, the measurements are stored in a controller which may transmit the measurements to a healthcare provider for assessment.