Employees' health conditions are issues for not only employees themselves but also companies and society to keep medical costs low and productivity high. In this analysis, 15,574 observations from 2,319 employees at four operational sites of a large corporation were used. The dataset contained physical and mental health conditions obtained from annual mandatory medical checkups, the Brief Job Stress Questionnaire (BJSQ), and work record information. Health and other factors related to long-term absenteeism (over three days in a quarter) were analyzed. Data were collected between February 2021 and January 2022, and we converted into quarterly observations. A logit (logistic regression) model was used in the analysis. Age and gender were identified as important basic characteristics. The estimates for these variables were positive and negative and significant at the 1% level. Among the variables obtained from the medical checkups, the estimates for diastolic blood pressure, HbA1c, anamnesis, heart disease history, smoking, increased weight, and frequency of alcohol consumption were positive and significant at the 1% level, further those for taking antihypertensive medications and kidney disease history were positive and significant at the 5% level. In contrast, the estimates for systolic blood pressure and amount of alcohol consumption were negative and significant at the 1% level. The estimate for taking antihyperglycemic medications and health guidelines were negative and significant at the 5% level. Among the variables obtained from the BJSQ, the estimates for amount of work felt, fatigue and support from family and friends were positive and significant at the 1%, and the estimate for irritation was positive and significant at the 5% level. The estimates for controlling job and physical complaints were negative and significant at the 1% level, and those for usage of employee's ability to work and suitability of the work were negative and significant at the 5% level. As all four operational sites were located in the northeastern region of Japan (cold and snowy in winter), the seasonal effects were significant at the 1% level. The effect of year was also significant and significant differences were observed among the sites at the 1% level. Some physical and mental health conditions were strongly associated with long-term absenteeism. By improving these conditions, corporations could reduce the number of employee absence days. As absenteeism was costly for corporations due to replacement employees and their training costs to maintain operations, employers must be concerned about rising healthcare (direct and indirect) costs and implement investments to improve employees' health conditions. This study's results were based on only one corporation and the dataset was observatory. The employees were primarily operators working inside the building and most of them are healthy. Therefore, the sample selection biases might exist, and the results cannot be generalized to other types of jobs, working conditions, or companies. As medical checkups and the BJSQ are mandatory for most companies in Japan, the framework of this study can be applied to other companies. Although we used the BJSQ results, better mental measures might exist. Similar analyses for different corporations are necessary.