Piroxicam is used to treat the pain, swelling, and stiffness associated with osteoarthritis and rheumatoid arthritis, but it has many side effects, such as hypertension, elevation of liver enzymes, and hepatitis. This study used selenium-enriched probiotics to reduce the side effects of piroxicam on the liver and kidney tissues and functions. Forty-eight male albino mice were randomly assigned to control, piroxicam (P), piroxicam plus selenium-enriched Lactobacillus plantarum PSe40/60/1 (P + SP), piroxicam plus selenium-enriched Bifidobacterium longum BSe50/20/1 (P + SB), selenium-enriched L. plantarum PSe40/60/1 (SP), and selenium-enriched B. longum BSe50/20/1 (SB) groups. In this study, the function of the liver and kidney was biochemically determined; the histopathology of the liver and kidney tissues was microscopically examined and the expression of inflammatory and anti-inflammatory genes in liver and kidney tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Liver and kidney functions were significantly reduced in the piroxicam group compared with control. Liver and kidney tissues were damaged in the piroxicam group while they appeared more or less normal in the SB group. The expression of inflammatory genes was significantly up-regulated in the liver and kidney tissues of the piroxicam group compared to the control group. The expression of anti-inflammatory genes was significantly down-regulated in the liver and kidney of the piroxicam group and up-regulated in the liver and kidney of the SB group compared to the control group. Therefore, these mutated strains of probiotics were useful in reducing the side effects of the piroxicam drug on the liver and kidney.