We have developed a simple method for the detection of live spirochaete stages in blood of patients where chronic borreliosis is suspected. Classic techniques involving phase-contrast and fluorescence microscopy are used. The method is also quite sensitive for detecting other bacteria, protists, fungi and other organisms present in blood samples. It is also useful for monitoring the effects of various antibiotics during treatment. We also present a simple hypothesis for explaining the confusion generated through the interpretation of possible stages of Borrelia seen in human blood. We hypothesize that these various stages in the blood stream are derived from secondarily infected tissues and biofilms in the body with low oxygen concentrations. Motile stages transform rapidly into cysts or sometimes penetrate other blood cells including red blood cells (RBCs). The latter are ideal hiding places for less motile stages that take advantage of the host’s RBCs blebbing-system. Less motile, morphologically different stages may be passively ejected in the blood plasma from the blebbing RBCs, more or less coated with the host’s membrane proteins which prevents detection by immunological methods.