It is important to recognize that subfertility may be contributed by both the male and female partners. Any assessment of the subfertile couple must therefore target both partners.
Components of Comprehensive Fertility Assessment are as follows:

A thorough clinical history taking is essential. Often, the fertility specialist would have a pretty good idea of the problem by noting down the menstrual cycle, presence of pelvic pain, difficulties with intercourse, past pelvic surgery and any symptoms suggestive of other medical conditions. For example, if the woman has irregular menstrual cycles, the problem is likely to be related to ovulation.
As for the male partner, any past history of surgery to the private part such as hernia or undecended testis is obtained. History of heavy smoking or drinking is also significant.
If the couple has previously sought fertility treatment elsewhere, it is important to review the records of previous treatments and investigations so that no unnecessary procedures are repeated.

A full physical examination and specifically an internal pelvic examination are performed. Often a woman who is over or underweight gives clues to what the problem is. Some overweight women have male features such as excessive facial hair and acne and are likely to have a condition called Polycystic Ovarian Syndrome (PCOS).
An internal examination is crucial to identify physical problems causing infertility, such as a large fibroid and a fixed position womb suggestive of scarring of the tubes. Sometimes tender nodules can be felt which could point to the presence of endometriosis.
It is rarely necessary to examine the man, unless the semen analysis is extremely abnormal. Examination concentrates on detecting small volume testicles or a condition called varicocele, where dilated testicular blood vessels lead to overheating of the testicles.
Ultrasound assessment of the pelvic organs is the cornerstone of fertility investigations. A properly conducted transvaginal ultrasound will identify most causes of infertility in the female. The shape and size of the womb as well as the regularity of the cavity of the womb is important. Sometimes the doctor may instill some fluid into the uterine cavity to have a better view. The appearance of the ovaries as well the number of potential eggs that are available (antral follicle count) gives us an idea of the woman's ovulation capability.
Occasionally, the woman undergoes an x-ray examination (hysterosalpingography) to assess the patency of the Fallopian tubes.

Generally, if the woman has a regular menstrual cycle, it is unnecessary to perform a blood hormonal profile as it does not offer any additional advantage. However in women with irregular cycles, age more than 38 and are suspected to have low ovarian reserves, a full hormonal profile which includes Follicular Stimulation Hormone (FSH), Luteinising Hormone (LH) and Oestradiol levels are performed.
A clomiphene citrate challenge test may be advised to further assess the ovarian reserve. This involves a baseline blood test and subsequently a course of fertility tablets called clomiphene to stimulate the ovaries before another blood test is repeated.
For couples with recurrent pregnancy losses or IVF failures, it may be necessary to run a battery of tests, which includes a screen of the couples chromosome make up (karyotyping).