Background Late-stage chronic kidney disease (LS-CKD) can be defined by glomerular filtration rate (GFR) 0–30 mL/min. It is a period of risk for medication discrepancies because of frequent hospitalizations, fragmented medical care, inadequate communication and polypharmacy. In this study, we sought to characterize medication discrepancies in LS-CKD. Methods We analyzed all patients enrolled in Northwell Health’s Healthy Transitions in LS-CKD program. All patients had estimated GFR 0–30 mL/min, not on dialysis. Medications were reviewed by a nurse at a home visit. Patients’ medication usage and practice were compared with nephrologists’ medication lists, and discrepancies were characterized. Patients were categorized as having either no discrepancies or one or more. Associations between patient characteristics and number of medication discrepancies were evaluated by chi-square or Fisher’s exact test for categorical variables, and two-sample t-test or Wilcoxon text for continuous variables. Results Seven hundred and thirteen patients with a median age of 70 (interquartile range 58–79) years were studied. There were 392 patients (55.0% of the study population) with at least one medication discrepancy. The therapeutic classes of medications with most frequently occurring medication discrepancies were cardiovascular, vitamins, bone and mineral disease agents, diuretics, analgesics and diabetes medications. In multivariable analysis, factors associated with higher risk of discrepancies were congestive heart failure [odds ratio (OR) 2.13; 95% confidence interval (CI) 1.44–3.16; P = 0.0002] and number of medications (OR 1.29; 95% CI 1.21–1.37; P