Advanced nanomaterials such as carbon nano-tubes (CNTs) display unprecedented properties such as strength, electrical conductance, thermal stability, and intriguing optical properties. These properties of CNT allow construction of small microfluidic devices leading to miniaturization of analyses previously conducted on a laboratory bench. With dimensions of only millimeters to a few square centimeters, these devices are called lab-on-a-chip (LOC). A LOC device requires a multidisciplinary contribution from different fields and offers automation, portability, and high-throughput screening along with a significant reduction in reagent consumption. Today, CNT can play a vital role in many parts of a LOC such as membrane channels, sensors and channel walls. This review paper provides an overview of recent trends in the use of CNT in LOC devices and covers challenges and recent advances in the field. CNTs are also reviewed in terms of synthesis, integration techniques, functionalization and superhydrophobicity. In addition, the toxicity of these nanomaterials is reviewed as a major challenge and recent approaches addressing this issue are discussed.