# Despite scientific advances in making microdialysis probes smaller and more efficient, the invasive nature of this technique still poses some practical and ethical limitations. For example, it has been shown that implantation of a microdialysis probe can alter tissue morphology resulting in disturbed microcirculation, rate of metabolism or integrity of physiological barriers, such as the blood–brain barrier. While acute reactions to probe insertion, such as implantation traumas, require sufficient recovery time, additional factors, such as necrosis, inflammatory responses, or wound healing processes have to be taken into consideration for long-term sampling as they may influence the experimental outcome. From a practical perspective, it has been suggested to perform microdialysis experiments within an optimal time window, usually 24–48 hours after probe insertion.
# Microdialysis has a relatively low temporal and spatial resolution compared to, for example, electrochemical biosensors. While the temporal resolution is determined by the length of the sampling intervals (usually a few minutes), the spatial resolution is determined by the dimensions of the probe. The probe size can vary between different areas of application and covers a range of a few millimeters (intracerebral application) up to a few centimeters (subcutaneous application) in length and a few hundred micrometers in diameter.
# Application of the microdialysis technique is often limited by the determination of the probe’s recovery, especially for in vivo experiments. Determination of the recovery may be time-consuming and may require additional subjects or pilot experiments. The recovery is largely dependent on the flow rate: the lower the flow rate, the higher the recovery. However, in practice the flow rate cannot be decreased too much since either the sample volume obtained for analysis will be insufficient or the temporal resolution of the experiment will be lost. It is therefore important to optimize the relationship between flow rate and the sensitivity of the analytical assay. The situation may be more complex for lipophilic compounds as they can stick to the tubing or other probe components, resulting in a low or no analyte recovery.