The study developed and applied an index for measuring the level of complexity of full authentic scientific inquiry. Complexity is a fundamental attribute of real life scientific research. The level of complexity is an overall reflection of complex cognitive and metacognitive processes which are required for navigating the authentic inquiry through high levels of uncertainty, from the unknown to the known. To develop the index, an educational framework was set up, in which five teams of high school students were conducting a full authentic scientific inquiry, using online facilitation. Protocols obtained from the teams' on-line communications were used for developing the Level of Complexity of Scientific Inquiry (LCSI) index. The index measures complexity by measuring the number of deviations from a linear straightforward inquiry process and the magnitude of these deviations. In structured teacher guided inquiries, the index measurement would be zero. The more students activate self-regulatory processes and grapple with the unknown, the higher is the obtained measurement.