After his studies at the major and minor seminary, Frans Alfons was ordained on September 18th 1886. Shortly afterwards he was sent to the Catholic University of Louvain to study Biology. In 1890 Janssens got his Doctoral degree in Natural Science. In 1891 he was awarded a scholarship for his thesis (Les branchies des Acéphales, published in 1893). With this money he was able to visit several laboratories of marine zoology abroad (Banyuls, Arachon, Den Helder, Naples and Roscoff). On July 14th 1891 he became a teacher in Math's and Natural Science at the St. Lieven institute in Gent. Then he was sent by his bishop to the brewery school in Munich and the famous brewery institute, Carlsberg, in Copenhagen, with a view to founding a brewery school in Gent. In Copenhagen, Janssens worked under J. Kjeldahl (inventor of the method of the same name to determine nitrogen in organic material) and E. C. Hansen (who developed a method for propagating yeast, very important in beer fermentation). Well educated, Janssens returned to Belgium, where he was a co-founder of the brewery school of the St. Lieven institute in Gent. In 1893 Janssens taught bacteriology there. Meanwhile he continued his scientific research in cytology.

On July 29th 1896, he started in Leuven as Professor at the Faculty of Sciences, where he taught Microscopy. In 1899, Janssens took over several courses of his predecessor, J. B. Carnoy, such as cytology, anatomy and physiology. At last he could concentrate fully on education and his scientific research.

Above all, Janssens was known as the "microscopy wizard". He fully mastered the technical side of the process as well as the preparation and coloration of the slides. People came from everywhere to consult him on difficulties they encountered in their research. He studied mostly the lower animal species, particularly mollusks and water salamanders. He also worked on yeast, fungi, frogs and toads. As a morphologist, he was "only" interested in the anatomy of the organisms he studied. He specialized in the description of cells, with a strong preference for the nucleus. His most famous discoveries concerned the chromosomes.

In 1909 he published La théorie de la chiasmatypie. The article contains only twenty-four pages, one page bibliography, two and half pages explanation of the drawings and three pages drawings of chromosomes in all their possible conformations. Janssens showed that, during meiosis, two homologous chromosome halves can approach and cross each other. At these particular sites, they partially break through at a different distance, exchange a little piece, and "grow" back together as two heterologous chromosome halves. It is as if small fragments of one chromosome are transferred to another chromosome. Janssens did no more then just observe and draw what happens at a very precise moment in the cell nucleus. Although severely attacked at that time by several colleagues, his theory has never been replaced by a more clear concept.

Janssens invented a new term to denote his discovery: chiasmatypie. Nowadays the term crossing-over is used worldwide (Dutch: overkruising; French: enjambement).

His discovery completely contradicted the opinions held at that time about the individuality of chromosomes. It was thought that there was only a remote possibility of exchange of small fragments between homologues chromosomes. F. A. Janssens however proved this in 1909. What did this discovery mean? It brought a more clear view on the laws of heredity, established by the Czech monk G. Mendel in 1865. The newly concieved individual bears chromosomes that differ from his parental chromosomes. The new individual is unique in the strictest sense possible.

Janssens discovery was gratefully used by T. H. Morgan in his Theory of linkage. Morgan immediately saw the great importance of Janssens cytological interpretation of chiasmata to the experimental results of his research on the heredity of Drosophila. Afterwards, a lot of effort was spent on chiasmatypie, especially by Wilson (1925), Sharp (1926-1943), Belar (1928), Guilliermond (1933), Darlington (1937) and Rhoades (1961). Janssens also went on with his research to further develop his theory.

Due to the first world war, Janssens had to give up teaching at the Catholic University of Leuven. He moved to Wichelen, where he installed a laboratory in his house. This way, he continued his scientific work, which resulted in another important publication in 1924, namely La chiasmatypie dans les insectes. During his last years, Janssens suffered greatly from ill health and became almost completely blind. He died in Wichelen, on October 8th, 1924.