The biomarkers that are observed and charted in fertility awareness based methods (FABMs) include:

1. Cervical mucus: The cervix is the lower part of the uterus and functions as the gateway between the vagina and the uterus. The cervix contains cervical crypts lined by cells that secrete cervical mucus. Different crypts secrete different types of mucus and respond to different hormonal influences. For most part of the female hormonal cycle, the mucus secreted by the cervix forms a plug that prevents sperm from entering the cervical canal and no cervical mucus appears at the vulva. Intercourse at this time cannot result in pregnancy. Under the influence of rising levels of estrogen that precede ovulation, the cervical mucus changes, allowing the entrance of sperm into the cervical canal. This kind of cervical mucus is recognisable at the vulva and intercourse at this time can result in pregnancy if ovulation takes place within the life span of sperm (3-5 days). By observing and charting the changes in their cervical mucus, a person can learn to identify the fertile and infertile phase of their cycle as well as gain information about the hormonal milieu that they are in. Mucus-only FABMs are based exclusively on the observation and charting of cervical mucus. All symptothermal and some symptohormonal methods also include observation and charting of cervical mucus.

2. Basal body temperature (BBT): The basal body temperature is a person’s lowest body temperature, attained during rest. The BBT rate reflects the body’s resting metabolic rate which is influenced by the female reproductive hormones. After ovulation, a corpus luteum is formed in the ovary. Corpus luteum is responsible for secreting high amounts of the hormone progesterone which among its many other functions, increases the body’s metabolic rate. This can be observed and charted as a rise in BBT. By measuring and charting their BBT a person can learn to more accurately identify the postovulatory infertile phase of the cycle.  Temperature-only FABMs are based on charting the basal body temperature and combining it to calculations or an algorithm. Symptothermal and some symptohormonal methods include charting the BBT but combine it to other biomarkers to accurately identify the infertile and fertile phases of the cycle.

3. Cervical changes: The cervix changes in position and texture throughout the menstrual cycle under the influence of fluctuating hormone levels. The cervix can be self-examined on a daily basis to observe for these changes. Many symptothermal FABMs teach the observation of cervical changes as an additional or alternative biomarker that can be helpful in situations where other observations are challenging to interpret.

4. Urinary hormone metabolites: Byproducts of the hormones that fluctuate during the menstrual cycle can be measured in the urine stream. Symptohormonal methods include measuring of hormone levels through urinary metabolites, most commonly the pituitary hormone LH which peaks before ovulation and estradiol which rises in the preovulatory phase of the cycle. Simple LH test strips or computerised monitors can be used to help to identify fertile and infertile phases of the cycle. 

5. Menstruation: Menstruation is charted as one biomarker in all FABMs. The first day of menstrual bleeding is considered the first day of the cycle. Calendar-based FABMs use menstruation as the only biomarker and estimate the fertile time of the menstrual cycle with calculations based on previous cycle lengths (the rhythm method) or assuming set cycle days as fertile when the menstrual cycle length is within normal ranges (the Standard Days method). Some symptohormonal FABMs add calculations based on previous cycle lengths or other cycle parameters to assess fertile time in the beginning of the cycle.