Fluorescence microscopy is a powerful imaging technique used in various scientific fields, particularly in biology and medicine, to visualize and study the distribution and behavior of molecules within cells and tissues. It exploits the phenomenon of fluorescence, which is attributed to various fluorophores or fluorescent dyes. As a part of this thesis, two new fluorescent BODIPY dyes were synthesized, containing substituents at the meso-position, specifically designed to target lysosomes or endoplasmic reticulum (ER). The synthetic strategy was based on the preparation of a BODIPY carboxylic acid, which was in the peptide coupling protocol in excellent yields attached to a morpholine residue or tosylsulphonamide derivative, respectively. Attempted synthesis of a BODIPY derivative with triphenylphosphonium salt to target mitochondria failed due to unsuccessful Williams ether synthesis of a BODIPY phenol with a bromoalkyne derivative. Spectral and photophysical properties were investigated in nonpolar (CH2Cl2), polar solvents – aprotic (CH3CN) and protic (H2O). The compounds have narrow and strong absorption (≈ 498 nm) and emission bands (510-515 nm) in the visible region and have small Stokes shifts. The compounds do not exhibit fluoro-solvatochromic properties, but the quantum yields of fluorescence (Φf = 0.50-0.75) decrease with increasing solvent polarity. Singlet excited state lifetimes were measured by timecorrelated single photon counting and they are in the nanosecond time-scale (τ = 2.6-3.0 ns). The fluorescence microscopy experiments were performed on the HFF cell line, demonstrating the easy internalization of the compounds and specific staining of lysosomes or ER at concentrations 5 μM and 1 μM, respectively. The obtained results suggest a potential application of the newly synthesized BODIPY compounds in medicine and biology as fluorescent indicators for targeting lysosomes and ER.