Microstructured waveguides with hollow core (HC-MOW) are of great interest for chemical and biological sensing. Due to the high overlap between a guiding light mode and an optical signal of analyte solution, filling of one or several fiber capillaries, such systems are able to provide strong sensitivity with respect to variations in the refractive index and the thickness of filling materials. Our approach is based on layer-by-layer assembly of oppositely charged polyelectrolytes with different molecular weights on the inner surface of HC-MOW. It was shown, the deposition of polyelectrolyte layers on the inner surface of hollow core causes a redshift in the transmission spectra. In particular, transmission shifts of up to 13 nm were detected for a multilayer polymer coating (5 bilayers).