The survival rate of severe illnesses and acute diseases depends on adequate and timely diagnosis and treatment. Unfortunately, many conditions only present noticeable symptoms during advanced stages, when it may be too late to treat. Furthermore, current diagnostic methods (e.g., biopsies) are intrusive, costly, and time-consuming to process in the lab, requiring patients to wait before treatment can start. To alleviate costs and waiting times for disease diagnostics, breath analysis can be applied at the point of care and is a promising technique and field of research. The European Union-funded project ‘VOCORDER’ aims to develop an infrared device capable of conducting rapid breath analysis tests on patients for continuous diagnostic and health monitoring, based on the volatile organic compound (VOC) profiles and metabolite biomarkers of patients’ breath. We present the study protocol for the VOCORDER project, which consists of two phases. Phase 1 is a baseline study aimed at detecting and identifying breath biomarkers for the early diagnosis of lung, stomach/colon, and breast cancers, as well as kidney insufficiency and acute infections (pneumonia). This phase employs ambient mass spectrometry (MS) and gas chromatography coupled with MS (GC-MS) to analyze breath samples from 120 healthy participants and 175 patients (35 per disease group). Phase 2 focuses on validating the newly developed portable breath analyzer in a cohort of 120 healthy controls and 100 patients with the above diseases. Breath samples were obtained in 1 L gas sampling bags at MITERA Hospital in Athens, Greece, and analyzed in the breath analysis laboratory at ETH Zürich, Switzerland, using secondary electrospray ionization high-resolution MS (SESI-HR-MS). The study protocol and preliminary breath metabolomic VOC data from patients with the targeted diseases are presented and discussed.