Background: More than 2 million people per year are treated for surgical wounds in the UK. Over a quarter of these wounds are estimated to heal by secondary intention (from the “bottom up”) resulting in further complications and requiring increased healthcare resources. Identification of microbiological or host biomarkers that can predict healing outcomes may help to optimize the management of surgical wounds healing by secondary intention. However, the microbial and host factor heterogeneity amongst this diverse population is completely unexplored. Methods: We demonstrate feasibility of determining presence and levels of wound microbes and systemic host factors in an inception cohort of 54 people presenting with surgical wounds healing by secondary intention, who were subsequently followed-up for a period of 12-21 months. We present descriptive statistics for plasma levels of inflammatory, angiogenic cytokines and microRNAs, and we identify a range of wound colonizing microbes. We tentatively explore association with healing aiming to generate hypotheses for future research. Results: We report a potential correlation between poor healing outcomes and elevated interleukin (IL)-6 plasma levels at presentation (ρ=0.13) which requires confirmation. Conclusions: This study demonstrates the degree of biological heterogeneity amongst people with surgical wounds healing by secondary intention and proves the feasibility of embedding a biomarker discovery study in a cohort study in surgical wounds. Our results are essential for designing large biomarker discovery studies to further investigate the potential validity of circulating IL-6 or other factors as novel predictive biomarkers of healing for surgical wounds healing by secondary intention.