The present invention relates to biochemistry, medicine, and molecular biology, in particular to analytical biochemistry and immunochemical assay, and is concerned with a biological microchip for multiple parallel detection and quantitative determination of different compounds. The biochip comprises an array of three-dimensional hydrogel elements which have a predetermined volume, formed on a support by the method of photo- or chemically induced polymerization, and containing biological molecules of the same or different nature (ligands). The invention provides a method for detecting compounds on the biological microchip, comprising identification thereof by mass spectrometry techniques directly on the hydrogel element of the microchip and a method for detecting immunoassay results, consisting in carrying an immuno-PCR and registering the results thereof on the same microchip. The invention also relates to a method of multiple parallel immunoassay of compounds on a biological microchip. Biological microchips for immunoassay and a method of carrying out multiple parallel analysis of compounds can find application in analyzing a wide range of high-molecular and low-molecular compounds, in medicine, pharmacology, food industry, environmental protection, in research work, particularly in proteomics.