Before main loop initializations take place, together with one shot actions during reset time. After that comes the main loop, where tasks are repeated over and over again. If for example you have a program that measures analog port and drives a LED according to the measured ADC value, then you would have a pseudocode as follows:
void main (void)
{
unsigned int anValue;
MakeLedPinOutput(); //initialize LED port pin
InitializeADC(); //Initialize analog port
while(1)
{
anValue = MeasureAnalogPort(); //get analog value
ControlLed(anValue); //drive LED accordingly
}
}