Professor Nilgun Baydogan's research focuses on the layers which ionizing radiation strikes on materials. Her working area encompasses the use of thin-film solar cells, flexible polymer nanocomposites, self-healing polymer nanocomposites, and living polymer in several industrial areas (for instance, aerospace applications, high altitude platforms to obtain high performance and radiation protection of optoelectronic equipment, and aircrew at the service area).

Her best-known works are the applications of nuclear techniques to several materials (such as polymer nanocomposites, semiconductors, thin-film solar cells, flexible materials, polymer and TCO thin films), optoelectronics and the applications of nondestructive methods (such as gamma-ray radiography, X-ray radiography and ultrasound testing) in several materials (such as polymer nanocomposites, stainless steels etc.).

The aim of using ionizing radiation in her research is to determine the suitable absorbed dose in materials to improve their performance in order for them to be utilised in satellites and aircraft, which requires a lot of attention to icephobic and hydrophobic coating, nanocomposites, nanocoatings with high corrosion resistance, and nanobiosensors for early diagnosis.