Proteins in general and secretory proteins in particular undergo posttranslational processes before they reach the structure in which they can fulfill their functional purpose. The protein precursor may undergo a wide variety of proteolytic cleavages, N- and C-terminal trimmings and amino acid derivatizations in cells that express the protein. Occasionally, the same precursor is differently processed in different cell types and, in addition, diseased cells may process a given precursor abnormally. For instance, the translational process is often either increased or decreased in diseased cells, which render the ensuing modifications of the precursor incomplete. As a result, a variable mixture of precursors and processing-intermediates accumulates. Measurement of a single protein or peptide component of the posttranslational processing cascade may not facilitate the diagnosis of a disease, because the pattern of precursors and processing products vary individually among patients. In order to exploit disturbed posttranslational processing for diagnostic use, and - at the same time - provide an accurate measure of the translational product, a simple analytical principle named “processing-independent analysis” (PIA) has been designed. PIA-methods quantitate the total mRNA product irrespective of the degree of precursor processing. PIA-methods have recently been developed for a number of prohormones and neuroendocrine proteins, and their diagnostic potential appears promising in early diagnosis of tumors and cardiovascular diseases. The present review describes posttranslational processing patterns for some neuroendocrine proteins. Second, PIA-measurements of precursor-products are mentioned with indication of problems and pitfalls. Finally, PIA-results obtained in diagnosis of neoplastic and cardiovascular diseases are highlighted. But first general aspects of the posttranslational processing are reviewed as a necessary basis for the understanding of the new diagnostic possibilities.