Microalbuminuria is closely associated with the risk of cardiovascular disease and all-cause mortality in the general population. Less is known about its relationship with subclinical atherosclerosis. We aimed to assess the prevalence of microalbuminuria and its relationship with subclinical atherosclerosis in middle-aged, nondiabetic, apparently healthy individuals (N = 187; 40.1% men, 59.9% women; aged 35–55 years) as well as to evaluate its potential associations with established risk modifiers, especially with the presence of carotid plaque. Clinical and laboratory parameters, the estimated 10-year fatal cardiovascular risk (SCORE), as well as circulating, functional (flow mediated vasodilation, ankle-brachial index, augmentation index, and pulse wave velocity), and morphological markers (mean carotid intima–media thickness, and carotid plaque) of subclinical atherosclerosis were analysed in group with vs. without microalbuminuria. Microalbuminuria was present in 3.8% of individuals with SCORE risk 0.43 ± 0.79%. Functional markers predominated in both groups. Carotid intima–media thickness (mean ± SD) in both groups was in range: 0.5–0.55 ± 0.09–0.14 mm. Carotid plaque was more frequent in group with (14.3%) vs. without (4.4%) microalbuminuria. Microalbuminuria had no statistically significant effect on most markers of subclinical atherosclerosis, but the increasing value of microalbuminuria was significantly associated with the occurrence of carotid plaque (p = 0.035; OR = 1.035; 95% CI = 1.002–1.07). Additional multiple logistic regression analysis, where variables belonged to microalbuminuria, number of risk factors, and family history, finally showed only two variables: microalbuminuria (p = 0.034; OR = 1.04; 95%CI = 1.003–1.09) and the number of risk factors (p = 0.006; OR = 2.15; 95% CI = 1.24–3.73) with independent and significant impact on the occurrence of carotid plaque. Our results may indicate an association of microalbuminuria with the presence of carotid atherosclerotic plaque; in addition, microalbuminuria and the number of risk factors appear to be possible predictors of the carotid plaque occurrence. Monitoring microalbuminuria may improve the personalized cardiovascular risk assessment in nondiabetic, low-to-moderate cardiovascular risk individuals with or without hypertension.