Non-saleable (waste) milk containing antibiotics is commonly fed to dairy calves. Effects of ingestion of antibiotics at an early age on the gut microbiome and the development of antibiotic resistance genes (ARG) in the naïve gut are unknown. Pirlimycin, a lincosamide active against gram-positive bacteria, is commonly used as mastitis therapy. Lincosamides are considered highly important in human medicine, with applications in S. aureus and C. difficile infections. Resistance to pirlimycin is emerging and is of concern for both animal and human health. The objective was to determine the effect of early antibiotic exposure on the abundance of ARG in feces of milk-fed calves. Eight female Holstein calves were assigned to pasteurized whole milk (control; n = 4) or milk containing 0.2 mg/L of pirlimycin (treatment; n = 4). Calves were enrolled after receiving 2 colostrum feedings, were blocked by age, and paired by block. Calves were fed 5.68 L of pasteurized whole milk, treatment or control, divided into 2 daily feedings, from d 1 to d 50 of age. After weaning at the age of 50 d, calves were fed ad libitum non-medicated starter grain. Fecal samples were collected weekly until 85 d of age and freeze-dried. DNA was extracted from all samples using QiaAmp Fast DNA Stool Mini Kit and qPCR was used to quantify the abundance (gene copies/g of wet feces) of TetW and 16S rRNA. Data were analyzed using PROC GLIMMIX in SAS. Differences were declared significant at P < 0.10, and trends at P < 0.15. Abundance of 16S rRNA was not different between control and pirlimycin-fed calves (mean = 9.81 log gene copies/g wet feces). Abundance of TetW tended to be higher (9.51 log gene copies/g wet feces; P = 0.13) in pirlimycin-fed calves compared with control calves. The relative abundance of TetW (0.49 gene copies/16S rRNA) in feces of calves was not influenced by treatment. Feeding pirlimycin-containing non-saleable milk to growing calves may increase environmental loading of TetW. Additional research is needed on effects on other ARG and on the post-excretion fate of these genes following application of manure from calves fed waste milk.