Detection of serum and urinary proteins is important for normal conditions, but comparison of individual serum and urine proteins is rarely performed. The aim of this study was to examine beta2-microglobulin (beta2-MG), apolipoprotein A-I (ApoA-I), and immunoglobulins (IgG and IgM) in the serum and urine of cats with chronic kidney disease and lower urinary tract disease (LUTD), in addition to healthy cats. Serum and urine samples were analyzed using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, followed by immunoblotting for beta2-MG, ApoA-I, IgG, and IgM. The molecular weight of serum beta2-MG was greater than the predicted molecular weight (11,472 Da), and different types of modified beta2-MGs were detected in the urine of healthy and diseased cats including original type in addition to grycocylated and partially digested types. Serum and urinary ApoA-I molecular weights were lower than the predicted molecular weight (28,943 Da), and high levels of urinary ApoA-I were detected in LUTD cats, although urinary ApoA-I was not detected in healthy cats. Under non-reducing conditions, H-chains of urinary IgM pentamers and IgG monomers were detected in healthy cats. These results suggest that urinary beta2-MG is modified in a different manner from serum beta2-MG, urinary ApoA-I is a potential marker of LUTD, and urinary IgM pentamer, IgG monomer, and their H-chains are found after glomerular filtration even in healthy conditions.