Epidemiological data indicate that metabolic disturbances and increased cardiovascular risk in renal transplant patients are a significant and common problem. Therefore, it is important to search for new solutions and, at the same time, counteract the negative effects of currently used therapies. In this study, we examined the effect of kidney transplantation on the serum levels of fatty acids (FAs) in order to assess the role of these compounds in the health of transplant patients. The FA profile was analyzed by gas chromatography-mass spectrometry in the serum of 35 kidney transplant recipients, just before transplantation and 3 months later. The content of total n-3 polyunsaturated FAs (PUFAs) decreased after transplantation (3.06 ± 0.13% vs. 2.66 ± 0.14%; < 0.05). The total amount of ultra-long-chain FAs containing 26 and more carbon atoms was significantly reduced (0.08 ± 0.009% vs. 0.05 ± 0.007%; < 0.05). The desaturation index (18:1/18:0) increased after transplantation (3.92 ± 0.11% vs. 4.36 ± 0.18%; < 0.05). The study showed a significant reduction in n-3 PUFAs in renal transplant recipients 3 months after transplantation, which may contribute to increased cardiovascular risk in this patient population.