Chronic kidney disease (CKD) is a progressive condition characterized by a permanent and irreversible loss of renal function. In accordance to international guidelines, CKD clinical diagnosis methods are based on creatinine and albumin levels and glomerular filtration rate. Unfortunately, these parameters are scarcely affected in early stages, and its inherent intrinsic variability only allows for the identification of intermediate and advanced stages, when life expectancy has become shorter and treatment poses a significant financial investment. In this context, several targeted strategies have been designed for searching novel markers. Among them, "omics" techniques have emerged, mainly based on proteomics and metabolomics research. Urine and serum samples have been selected as starting material to conduct the identification of new CKD biomarkers, capable of differentiating between stages and predicting progression outcomes. In many cases, the principal objective is to develop a fast and reliable clinical method for non-invasive analysis in the early progression stages of the disease. On the other hand, significant efforts have been directed to identify molecules related to the CKD end stage in order to adequate therapies, reduce impairments, and have a positive impact on survival rate. In this article, the state of the art of novel proposed biomarkers for CKD identification is reviewed, with the aim of underlining its molecular diversity, emphasizing chemical structure differences and correlating its biological relevance. Efforts directed in this line could provide evidence of metabolic pathways imbalance, and lead to the development of new integral strategies for CKD evaluation and management.