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MicroRNAs (miRNAs) have demonstrated their potential as biomarkers for diagnostic purposes and disease monitoring in a wide variety of studies. Particularly desirable is the detection of specific miRNA fingerprints in patients from easily-accessible samples such as body fluids rather than from tissue biopsies. We measured miRNA profiles in different body fluids like whole-blood and blood serum of more than 1,000 patients suffering from a variety of diseases. These included tumors such as lung carcinoma, pancreatic cancer and prostate cancer as well as inflammatory diseases like multiple sclerosis, pancreatitis and COPD. The microarrays used for miRNA profiling in these studies contained all miRNA sequences as annotated in miRBase version 12.0 or higher. To extract relevant information from this large data set we implemented a miRNA database. This database contains the miRNA profile along with clinical information for each sample, such as the TNM status of a cancer patient. miRNA profiles from different diseases and controls can be extracted and analyzed. In addition, the profiles can be used for classifying patients based on the developed biomarker signatures. Besides the comparison of diseases and controls, numerous relevant diagnostic tasks can be addressed, for example distinguishing between lung cancer and COPD patients, or identifying putative differences between metastasizing and non-metastasizing cancers. In summary, we collected the largest set of complex miRNA profiles from patients’ body fluids. Our data will help scientists and clinicians alike to address many questions of different nature.